Variant report

Variant	rs11902653
Chromosome Location	chr2:167997478-167997479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr2:167997098-167997814	ECC-1	luminal epithelium:	n/a	chr2:167997412-167997421
2	STAT3	chr2:167997178-167997644	MCF10A-Er-Src	breast:	n/a	chr2:167997321-167997332
3	USF1	chr2:167997226-167997698	ECC-1	luminal epithelium:	n/a	n/a
4	TAF1	chr2:167997308-167997645	SK-N-SH	brain:	n/a	n/a
5	JUND	chr2:167997053-167997893	SK-N-SH	brain:	n/a	n/a
6	USF1	chr2:167997285-167997604	SK-N-SH_RA	brain:	n/a	n/a
7	TEAD4	chr2:167997011-167997838	SK-N-SH	brain:	n/a	chr2:167997412-167997421
8	NFIC	chr2:167997134-167997710	SK-N-SH	brain:	n/a	n/a
9	FOXM1	chr2:167997134-167997689	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr2:167997165-167997746	ECC-1	luminal epithelium:	n/a	chr2:167997412-167997421
11	MAX	chr2:167997266-167997857	HCT-116	colon:	n/a	chr2:167997583-167997590 chr2:167997508-167997517
12	FOS	chr2:167997213-167997733	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr2:167997278-167997513	SK-N-SH	brain:	n/a	n/a
14	JUND	chr2:167996969-167998219	SK-N-SH	brain:	n/a	n/a
15	USF1	chr2:167997225-167997649	SK-N-SH	brain:	n/a	n/a
16	EP300	chr2:167997209-167997657	SK-N-SH_RA	brain:	n/a	n/a
17	POLR2A	chr2:167997101-167997658	HUVEC	blood vessel:	n/a	n/a
18	FOXM1	chr2:167997212-167997924	ECC-1	luminal epithelium:	n/a	n/a
19	E2F4	chr2:167997293-167997728	MCF10A-Er-Src	breast:	n/a	n/a
20	RCOR1	chr2:167996872-167997829	IMR90	lung:	n/a	n/a
21	MAX	chr2:167997130-167997878	ECC-1	luminal epithelium:	n/a	chr2:167997583-167997590 chr2:167997508-167997517
22	NFIC	chr2:167997109-167997903	ECC-1	luminal epithelium:	n/a	n/a
23	MYC	chr2:167997141-167997883	MCF10A-Er-Src	breast:	n/a	chr2:167997583-167997590 chr2:167997508-167997517
24	TCF12	chr2:167997260-167997798	ECC-1	luminal epithelium:	n/a	chr2:167997446-167997456
25	FOSL2	chr2:167997035-167997815	SK-N-SH	brain:	n/a	n/a
26	USF1	chr2:167997304-167997758	ECC-1	luminal epithelium:	n/a	n/a
27	MAX	chr2:167997295-167997786	HCT-116	colon:	n/a	chr2:167997583-167997590 chr2:167997508-167997517
28	PBX3	chr2:167997091-167997670	SK-N-SH	brain:	n/a	n/a
29	GATA3	chr2:167996968-167997883	SK-N-SH	brain:	n/a	n/a
30	EP300	chr2:167996881-167997912	SK-N-SH	brain:	n/a	n/a
31	USF1	chr2:167997251-167997676	HCT-116	colon:	n/a	n/a
32	SIN3AK20	chr2:167997272-167997481	PFSK-1	brain:	n/a	n/a
33	FOS	chr2:167997171-167997698	MCF10A-Er-Src	breast:	n/a	n/a
34	TCF12	chr2:167997063-167997831	ECC-1	luminal epithelium:	n/a	chr2:167997446-167997456
35	EP300	chr2:167997135-167997693	SK-N-SH_RA	brain:	n/a	n/a
36	RXRA	chr2:167997116-167997842	SK-N-SH	brain:	n/a	chr2:167997323-167997332
37	FOSL1	chr2:167997150-167997720	HCT-116	colon:	n/a	n/a
38	POLR2A	chr2:167997141-167997671	SK-N-SH	brain:	n/a	n/a
39	YY1	chr2:167997177-167997783	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr2:167997322-167997586	PFSK-1	brain:	n/a	n/a
41	JUND	chr2:167997162-167997629	HCT-116	colon:	n/a	n/a
42	MEF2A	chr2:167996971-167997877	SK-N-SH	brain:	n/a	chr2:167997592-167997607 chr2:167997700-167997716 chr2:167997265-167997286 chr2:167997700-167997717
43	EP300	chr2:167996970-167997858	SK-N-SH	brain:	n/a	n/a
44	MEF2A	chr2:167997020-167997901	SK-N-SH	brain:	n/a	chr2:167997592-167997607 chr2:167997700-167997716 chr2:167997265-167997286 chr2:167997700-167997717
45	TAF1	chr2:167997133-167997647	PFSK-1	brain:	n/a	n/a
46	TEAD4	chr2:167996985-167997812	SK-N-SH	brain:	n/a	chr2:167997412-167997421
47	CEBPB	chr2:167997151-167997629	IMR90	lung:	n/a	n/a
48	USF1	chr2:167997290-167997627	SK-N-SH_RA	brain:	n/a	n/a
49	POLR2A	chr2:167997292-167997533	MCF10A-Er-Src	breast:	n/a	n/a
50	ESR1	chr2:167997266-167997609	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
XIRP2-AS1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10451542	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1155284	0.93[CEU][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs1155285	0.88[EUR][1000 genomes]
rs11888230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11893377	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11893404	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11893509	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1346722	0.82[CEU][hapmap]
rs1479592	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs16853050	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs16853057	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4000962	0.84[EUR][1000 genomes]
rs4533448	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.84[LWK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55733637	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58616240	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59504679	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6432979	0.89[EUR][1000 genomes]
rs66701411	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67074513	0.89[EUR][1000 genomes]
rs6711844	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs6720352	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs6720763	1.00[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67386767	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67485531	0.82[EUR][1000 genomes]
rs67726376	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68108130	0.81[EUR][1000 genomes]
rs73017939	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556854	0.92[CHD][hapmap];0.95[GIH][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7569147	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7575729	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs988445	1.00[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs998899	0.93[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875376	chr2:167844513-168037489	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:167989200-167998600	Weak transcription	Left Ventricle	heart
2	chr2:167992200-167999800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:167993800-167999800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:167995000-167999400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:167995000-167999600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:167996200-167998200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:167996200-167998400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:167996200-167998600	Enhancers	HMEC	breast
9	chr2:167996200-168001400	Enhancers	Fetal Heart	heart
10	chr2:167996200-168001400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:167996600-167998200	Enhancers	HSMM	muscle
12	chr2:167996600-167998200	Enhancers	NHEK	skin
13	chr2:167996800-167997600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:167996800-167997600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr2:167996800-167998000	Enhancers	NH-A	brain
16	chr2:167996800-167998000	Enhancers	NHDF-Ad	bronchial
17	chr2:167996800-167998200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:167996800-167998200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:167996800-167998200	Enhancers	Osteobl	bone
20	chr2:167997000-167998000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:167997000-167998200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:167997000-167999200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:167997200-167997600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:167997200-167997600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:167997200-167997800	Enhancers	Rectal Smooth Muscle	rectum
26	chr2:167997200-167998600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:167997200-167999400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:167997200-167999600	Weak transcription	Psoas Muscle	Psoas
29	chr2:167997400-167997800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:167997400-167999600	Weak transcription	NHLF	lung
31	chr2:167997400-168001000	Enhancers	Skeletal Muscle Male	skeletal muscle

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